The Cellar - Cellar car issue

I can't merge with the other car threads, that would be wrong.

I'm facing the hardest of all car problems... the electrical. I thought maybe summing it up here would get all the facts in order. But first a little history!

The Cellar Car was delivered with the issue of the right rear window being unable to roll all the way up. It was stuck 2.5" (4 cm) from the top.

This was solved in the short order: with duct tape. Put tape across the opening until no air or water will get in, and that's good enough. The only time the duct tape failed was during the folk fest, when it was left in direct sun all day, and the adhesive melted. To resolve this issue, I located a duct tape that was rated for high temperatures, as if when used on actual ducts. This higher temperature tape proved to work well when the next folk fest rolled around, and I was satisfied.

Then one day J's kid was looking for something to do, so I thought I'd be generous, and give him the work of opening up the door and putting the window in the full upright position. I figured maybe he could jam a 2x4 in there to keep it in place. I didn't care whether it went up and down.

But then the kid's friend comes around, and they're both wrenchers; so they get interested in fixing the whole thing properly. So I give them $40, and they go down to the junkyard and fetch the right window motor to actually move the window up and down.

They come back and fix the goddamn thing 100%, a fine day's work. But in the process of doing all this, they somehow run the battery down; and so at one point they jumpstart it and leave it running awhile to charge the battery.

But the next day, I find that the stereo is just dead. Display won't light up, it's just dead.

Online, people say that sometimes a dead battery does seem to kill this model of stereo, and jumpstarting might just make things worse. I check the car's fuse marked AUDIO, and it's fine, and I check the two fuses running into the stereo as part of the wiring harness, and they're both fine. So I figure the thing is just dead and I have to replace it.

Six months later and I finally find on eBay a "factory refurbished" unit cheap, not my model but one that uses the exact same wiring harness. So I figure this'll be great, I won't have to change out the harness, just slide this new unit in and it'll all work great.

So I get this new unit, and plug it into the old harness... DEAD! Except for one thing: when I hit the CD Eject button, it makes that little eject sound even though there is no CD in it.

Weird. Goddamn.

So I unplug it, and the next day I try it again. And this time when I plug it in, the car tries to raise the rear antenna with its antenna motor. It can't accomplish that, the antenna is bent and won't raise. But it tries for a moment. The whole thing is still dead, and now it won't even make the CD Eject sound.

One other clue. Located just above the stereo are the controls for heating/air conditioning. These controls are lit and a little LED lights up under each button to tell you whether your vents are pointing at your legs or at your face, and such. Well at some point those buttons stopped lighting. The LEDs work, but the lights for the icons are not lit. I don't know whether that has anything to do with it all.